├── INSTALL.sh ├── README.md ├── appveyor.yml ├── conda.recipe └── meta.yaml ├── geneLift.py ├── geneLift ├── __init__.py ├── __main__.py ├── _version.py ├── add_utrs_to_gff.py ├── bed_to_gff_converter.py ├── cli.py ├── remove_overlapping_genes.py ├── scripts │ ├── filter_gmap_gff3.sh │ ├── filter_minimap2_gff3.sh │ ├── filter_overlaps_minimap2_gff3.sh │ ├── format_child_ids.sh │ ├── format_func_gff3.sh │ ├── format_func_minimap2_gff3.sh │ ├── format_gmap_gff3.sh │ ├── format_minimap2_gff3.sh │ ├── map_gff_ids.pl │ ├── remove_failed_genes.sh │ ├── remove_note_from_genes.sh │ ├── update_func_gff │ └── validate_and_correct.sh └── utils.py ├── gmap_pipeline.py ├── minimap2_pipeline.py ├── setup.cfg ├── setup.py ├── test_data ├── annot.txt ├── cDNA.fasta └── test.fasta ├── tests ├── __init__.py └── test_cli.py └── versioneer.py /INSTALL.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/srividya22/geneLift/HEAD/INSTALL.sh 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